The spatio-temporal evolution of the energetic particles in the transport time scale in tokamak plasmas is a key issue of the plasmas confinement, especially in burning plasmas. In order to include sources and sinks and collisional slowing down processes, a new solver, ATEP-3D was implemented to simulate the evolution of the EP distribution in the three-dimensional constants of motion (CoM) space. The Fokker-Planck collision operator represented in the CoM space is derived and numerically calculated. The collision coefficients are averaged over the unperturbed orbits to capture the fundamental properties of EPs. ATEP-3D is fully embedded in ITER IMAS framework and combined with the LIGKA/HAGIS codes. The finite volume method and the implicit Crank-Nicholson scheme are adopted due to their optimal numerical properties for transport time scale studies. ATEP-3D allows the analysis of the particle and power balance with the source and sink during the transport process to evaluate the EP confinement properties.